ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals

The chromatin remodelling enzymes SNF2H and SNF2L position nucleosomes adjacent to CTCF and other transcription

Within the genomes of metazoans, nucleosomes are highly organised adjacent to the binding sites for a subset of transcription factors. Here we have sought to investigate which chromatin remodelling enzymes are responsible for this. We find that the ATP-dependent chromatin remodelling enzyme SNF2H plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding. At many other factor binding sites SNF2H and the related enzyme SNF2L contribute to nucleosome organisation. The action of SNF2H at CTCF sites is functionally important as depletion of CTCF or SNF2H affects transcription of a common group of genes. This suggests that chromatin remodelling ATPase's most closely related to the Drosophila ISWI protein contribute to the function of many human gene regulatory elements

Ectopic hbox12 Expression Evoked by Histone Deacetylase Inhibition Disrupts Axial Specification of the Sea Urchin Embryo

Dorsal/ventral patterning of the sea urchin embryo depends upon the establishment of a Nodal-expressing ventral organizer. Recently, we showed that spatial positioning of this organizer relies on the dorsal-specific transcription of the Hbox12 repressor. Building on these findings, we determined the influence of the epigenetic milieu on the expression of hbox12 and nodal genes. We find that Trichostatin-A, a potent and selective histone-deacetylases inhibitor, induces histone hyperacetylation in hbox12 chromatin, evoking broad ectopic expression of the gene. Transcription of nodal concomitantly drops, prejudicing dorsal/ventral polarity of the resulting larvae. Remarkably, impairing hbox12 function, either in a spatially-restricted sector or in the whole embryo, specifically rescues nodal transcription in Trichostatin-A-treated larvae. Beyond strengthen the notion that nodal expression is not allowed in the presence of functional Hbox12 in the same cells, these results highlight a critical role of histone deacetylases in regulating the spatial expression of hbox12

Defining functional DNA elements in the human genome

With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease

Nephrostomy-free percutaneous nephrolithotripsy: intraoperative hemostasis methods of the percutaneous tract

Review based on the analysis of more than 40 scientific papers published in the Pubmed and Medline databases from 1984 to 2019, dedicated to intraoperative hemostasis of the percutaneous tract and its tightness during nephrostomyfree percutaneous nephrolithotomy (PCNL). The article aimed to summarize scientific data on this issue. We presented information about the history and development of percutaneous surgery in the treatment of urolithiasis. In our review, we have been demonstrated various methods of surgical and intraoperative hemostasis during nephrostomy-free PCNL

Alterações eletrocardiográficas na intoxicação aguda por antidepressivo tricíclico e suas implicações clínicas

Introduction: The acute poisoning by tricyclic antidepressants is common in emergency rooms. Abnormalities in 12-lead electrocardiogram (ECG) are associated with this type of poisoning, with diagnostic and prognostic implications. The ECG may have incremental value especially in situations of altered consciousness, seizures or heart rhythm disturbances associated. Objective: To review the electrocardiographic changes described in tricyclic antidepressant poisoning and to establish their prognostic implications in the management of this condition. Methods: Bibliographic search in MEDLINE (PubMed) limited to articles published between 1980 and 2010 in English, using key words (tricyclic antidepressant overdose OR tricyclic antidepressant intoxication OR tricyclic antidepressant poisoning OR tricyclic antidepressant ingestion AND electrocardiography). Of the 133 articles identified, 44 were selected for review. Results: We identified prevalent as changes with diagnostic power in descending order the following findings: deviation of 40 ms terminal of QRS to the right of the frontal plane (from 61.0 to 83.0%), sinus tachycardia (40.7 to 57.7 %), QTc prolongation (8.2 to 53.0%), ratio R / S in aVR> 0.7 (28.8 to 32.9%), prolongation of QRS (8.2 to 21.3% ) and Brugada-pattern, the evidence is sparse, but suggestive of a greater chance of seizures and hypotension. Conclusion: The ECG is an instrument easily performed in the emergency room, providing diagnostic and prognostic information for poisoning by tricyclic and should be performed in all patients with suspicion of intoxicationIntrodução: A intoxicação aguda por antidepressivos tricíclicos é comum nas salas de emergência. Anormalidades no eletrocardiograma de 12 derivações (ECG) são associadas a este tipo de intoxicação, com implicações diagnósticas e prognósticas. O ECG pode ter valor incremental principalmente em situações de alteração de consciência, convulsões ou distúrbios do ritmo cardíaco associado. Objetivo: Revisar as principais alterações eletrocardiográficas descritas na intoxicação por antidepressivos tricíclicos e estabelecer suas implicações prognósticas no manejo desta condição clínica. Metodologia: Pesquisa bibliográfica no MEDLINE (PubMEd) limitada aos artigos publicados entre 1980 e 2010 em língua inglesa, utilizando-se unitermos (tricyclic antidepressant overdose OR tricyclic antidepressant intoxication OR tricyclic antidepressant poisoning OR tricyclic antidepressant ingestion AND electrocardiography). Dos 133 artigos identificados, foram selecionados 44 para a revisão.  Resultado: Foram identificados como alterações prevalentes com poder diagnóstico em ordem decrescente os seguintes achados: desvio dos 40 ms terminais do QRS para a direita do plano frontal (61,0-83,0%), taquicardia sinusal (40,7-57,7%), prolongamento do QTc (8,2-53,0%),relação R/S em aVR>0,7 (28,8-32,9%), prolongamento do QRS (8,2-21,3%) e padrão Brugada-like (2,3-15,3%).  Destes achados, somente o prolongamento do QRS foi prognóstico para morte, convulsão e arritmia e o prolongamento do QTc e a relação R/S em aVR>0,7 para arritmia ventricular. Para o padrão Brugada-like , as evidências são escassas, mas sugestivas de maior chance de convulsão e hipotensão. Conclusão: O ECG é um instrumento de fácil realização na sala de urgência, fornecendo informações diagnósticas e prognosticas para a intoxicação por tricíclicos, devendo ser realizado em todo paciente com suspeita desta intoxicação.

Myocardial ultrasonic tissue characterization in patients with thyroid dysfunction

<p>Abstract</p> <p>Background</p> <p>Structural myocardial abnormalities have been extensively documented in hypothyroidism. Experimental studies in animal models have also shown involvement of thyroid hormones in gene expression of myocardial collagen. This study was planned to investigate the ability of ultrasonic tissue characterization, as evaluated by integrated backscatter (IBS), to early identify myocardial involvement in thyroid dysfunction.</p> <p>Patients and Methods</p> <p>We studied 15 patients with hyperthyroidism (HYPER), 8 patients with hypothyroidism (HYPO), 14 patients with subclinical hypothyroidism (SCH) and 19 normal (N) subjects, who had normal LV systolic function. After treatment, 10 HYPER, 6 HYPO, and 8 SCH patients were reevaluated. IBS images were obtained and analyzed in parasternal short axis (papillary muscle level) view, at left ventricular (LV) posterior wall. The following IBS variables were analyzed: 1) the corrected coefficient (CC) of IBS, obtained by dividing IBS intensity by IBS intensity measured in a rubber phantom, using the same equipment adjustments, at the same depth; 2) cardiac cyclic variation (CV) of IBS - peak-to-peak difference between maximal and minimal values of IBS during cardiac cycle; 3) cardiac cyclic variation index (CVI) of IBS - percentual relationship between the cyclic variation (CV) and the mean value of IBS intensity.</p> <p>Results</p> <p>CC of IBS was significantly larger (p < 0.05) in HYPER (1.57 ± 0.6) and HYPO (1.53 ± 0.3) as compared to SCH (1.32 ± 0.3) or N (1.15 ± 0.27). The CV (dB) (HYPO: 7.5 ± 2.4; SCH: 8.2 ± 3.1; HYPER: 8.2 ± 2.0) and the CVI (HYPO: 35.6 ± 19.7%; SCH: 34.7 ± 17.5%; HYPER: 37.8 ± 11.6%) were not significantly different in patients with thyroid dysfunction as compared to N (7.0 ± 2.0 and 44.5 ± 15.1%).</p> <p>Conclusions</p> <p>CC of IBS was able to differentiate cardiac involvement in patients with overt HYPO and HYPER who had normal LV systolic function. These early myocardial structural abnormalities were partially reversed by drug therapy in HYPER group. On the other hand, although mean IBS intensity tended to be slightly larger in patients with SCH as compared to N, this difference was not statistical significant.</p

Ethylene receptor ETR2 controls trichome branching by regulating microtubule assembly in Arabidopsis thaliana

The single-celled trichome of Arabidopsis thaliana is a widely used model system for studying cell development. While the pathways that control the later stages of trichome development are well characterized, the early signalling events that co-ordinate these pathways are less well understood. Hormones such as gibberellic acid, salicylic acid, cytokinins, and ethylene are known to affect trichome initiation and development. To understand the role of the plant hormone ethylene in trichome development, an Arabidopsis loss-of-function ethylene receptor mutant, etr2-3, which has completely unbranched trichomes, is analysed in this study. It was hypothesized that ETR2 might affect the assembly of the microtubule cytoskeleton based on analysis of the cytoskeleton in developing trichomes, and exposures to paclitaxol and oryzalin, which respectively act either to stabilize or depolymerize the cytoskeleton. Through epistatic and gene expression analyses it is shown that ETR2 is positioned upstream of CHROMATIN ASSEMBLY FACTOR1 and TRYPTICHON and is independent of the GLABRA2 and GLABRA3 pathways. These results help extend understanding of the early events that control trichome development and identify a signalling pathway through which ethylene affects trichome branching

Penile and scrotum entrapment by a metal ring with pressure sore formation: a clinical case report

Penile entrapment is a rather rare pathology and requires urgent treatment to preserve the organ function. The article presents a clinical case of entrapment of the penile root and scrotum by a metal ring with tissue changes like a pressure sore directly under the ring. Possible methods of emergency surgical treatment in this urgent situation are discussed